Transcript The Great Clade Race

The Great Clade Race
Tree-thinking activities for marine
scientists
Susan L. Richardson, Ph.D.
Wilkes Honors College, Florida Atlantic University
Teaching Oceanography Workshop: 18-20 June 2013
Why Tree-thinking?
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Understanding how to
interpret phylogenetic, or
evolutionary trees, is an
essential skill in modern
biology.
Trees are generated from
computer analyses of
morphological
(phenotypic characters)
and/or molecular
sequence (DNA, RNA,
etc.) data sets.
Phylogenetic tree of 3,000 species:
<1% of known species are depicted
http://www.utexas.edu/features/2008/tree/
Fish
supper
Mosses
Cornflakes are
here
Animals
Plants
You are
here
Athlete’
s foot
Cotton
socks
“Protists”
Fungi
Bacteria
Muséum nationale d’Histoire Naturelle (Paris)
Why Tree-thinking?
Evolution underlies biological diversity
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Most current biology
textbooks portray the
evolutionary relationships
of organisms in the form
of phylogenetic trees.
Life in modern oceans is
more abundant and
diverse than on land.
Life evolved in the ocean
and radiated to
freshwater and terrestrial
habitats.
“Water” by Giuseppe Arcimboldo (1566)
Why Tree-thinking?
Tree of Life
Why Tree-thinking?
Unculturable Marine Microbes
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Environmental sequencing of
seawater has illuminated the
vast diversity of genes in the
ocean.
Some groups of marine
microbes (and viruses) are
only known from gene
sequences.
Craig Venter on Sorcerer II
http://ucsdnews.ucsd.edu/thisweek/2006/oct/10_16_venter.asp
Why Tree-thinking?
Unculturable Marine Microbes
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Some groups of marine
microbes are only known from
gene sequences
The SAR11 clade is a group
of alpha-proteobacteria
identified primarily from
ribosomal gene sequences
identified in DNA extracted
from seawater.
The global biomass of SAR11
bacteria is greater than all the
fish in the ocean; their
abundance is estimated to be
2.4 X 1028 SAR11 bacterial
cells in ocean.
Brown et al. (2012). Global biogeography of SAR11 marine bacteria: Molecular Systems Biology, 8: 595.
Why Tree-thinking?
Conservation Applications
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Trees are used in marine
conservation biology to
identify illegally harvested
marine life.
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Legal: Minke whales;
fin whales?
Illegal: Humpback
whales; dolphins
er & Palumbi (1994). Which whales are hunted? A molecular genetic approach to monitoring whaling: Science, v. 265, p. 1538-15
Why Tree-thinking?
Conservation Applications
•
Witness for the Whales is
a service for the
identification of cetaceans
(whales, dolphins and
porpoises) using DNA
sequences.
http://www.cebl.auckland.ac.nz:9000/page/wftw/intro
Why Tree-thinking?
Conservation Applications
•Sequence 1
•>Unknown1
•GAAAATATATATTGTACAATAACCACAAGGCCACAGTATTATGTCCGT
ATTAAAAATAACTTATTTTATTGCATACTGTTATGTAACTTGTGCATGTA
TGTACTCCCACATAACCCATAGTAGTTAGTATTCCCCTGTGAATATGT
ATATGTACACATACTATGTATAATTGTGCATTCAATTATCTTCACTACG
GAAGTTAAAGCCCGTATTAAATTTTATTAATTTTACATATTACATAATAT
TTATTAATAGTACAATAGTACATGTTCTTATGCATCCTCAGGTCATTCT
AGACGGAATGACTCTTATGGCCGCTCCATTAGATCACGAGCTTAATCA
GCATGCCGCGTGAAACCAGCAACCCGCTCGGCAGGGATCCCTCTTC
TCGCACCGGGCCCATCAATCGTGGGGGTAGCTATTTAATGATCTTTAT
AAGACATCTGGTTCTTACTTCAGGACCATATTAACTTAAAATCGCCCA
CTC
http://www.cebl.auckland.ac.nz:9000/page/whales/title
http://www.cebl.auc
kland.ac.nz:9000/pa
ge/whales/title
http://www.cebl.auckland.ac.nz:9000/page/wftw/methods
ID’d as gray whale
Why Tree-thinking?
Trees show evolutionary trends
Lim et al. (2010) . Phylogeny of hammerhead sharks (Family Sphyrinidae) inferred from
mitochondrial and nuclear genes. Mol. Phylog. & Evol. 55: 572-579.
The Great Clade Race
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These cards represent cards
carried by eight runners in an
imaginary race through the
woods.
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The racecourse is made of
diverging paths. As runners
encounter a fork in the path,
they choose to go to the right
or the left, and continue in this
manner to the finish line.
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Although each runner starts
the race at the same place,
each runner finishes the race
at a separate finish line.
Goldsmith (2003). The Great Clade Race. American Biology Teacher 65(9):679-682.
The Great Clade Race
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Along the stretches between
the forks in the path are
check-in stations; each checkin station has a unique stamp.
As runners pass a station,
they stop to collect a stamp on
their card.
Using the collections of
stamps on each card,
students must reconstruct the
pattern of the racecourse that
shows: the forks in the path,
the location of the check-in
stations & the finish line for
each runner.
The Great Clade Race
Rules
1. All runners must complete the
race. They cannot drop out of
the race.
2. When the path branches, it
only branches into two new
paths, never three or more.
3. Once two paths have
branched off from one
another, they can never
reconnect.
4. Check-in stations along the
legs between the forks in the
path.
Work in groups to map out the
“racecourse” for the Great Clade
Race.
The Great Clade Race
Correct Trees
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There are several correct
trees that contain the same
information.
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The pattern of branching is
what is relevant; branches
can be rotated around
each node and still portray
the same information.
Branch length is not
important for our example.
Shape (square, curved, etc.)
of trees is not important;
orientation is not important.
The Great Clade Race
One Correct Tree
The Great Clade Race
Another Correct Tree
Runners 1-4
Alternative “tree” topologies
Runners 1-4
Alternative “tree” topologies
Runners 5-8
Alternative “tree” topologies
Examples of Student
Trees